Man pages for PREDA
Position Related Data Analysis
| analysesNames | Get the names of the analyses in the from PREDA objects |
| computeDatasetSignature | Function to compute dataset signature for recurrent... |
| DataForPREDA2dataframe | extract data and annotations as a dataframe |
| DataForPREDA2GenomicAnnotationsForPREDA | extract a GenomicAnnotationsForPREDA object from a data... |
| DataForPREDA2StatisticsForPREDA | extract a StatisticsForPREDA object from a data DataForPREDA... |
| DataForPREDA-class | Class "DataForPREDA" is used to manage all of the data... |
| DataForPREDAMedianCenter | Function to scale median value of DataForPREDA statistics to... |
| eset2GenomicAnnotations | Function building a GenomicAnnotations object on an... |
| genomePlot | draw a genome plot |
| GenomicAnnotations2dataframe | extracts annotations as a dataframe |
| GenomicAnnotations2GenomicAnnotationsForPREDA | generate a GenomicAnnotationsForPREDA object from a... |
| GenomicAnnotations2reference_positions | extract reference positions from the GenomicAnnotations |
| GenomicAnnotations-class | Class "GenomicAnnotations" to manage information about... |
| GenomicAnnotationsExtract | extract optional annotations for a specific region |
| GenomicAnnotationsFilter_neg | filter annotations to remove selected chromosomes |
| GenomicAnnotationsFilter_pos | filter annotations to keep selected chromosomes |
| GenomicAnnotationsForPREDA2dataframe | extract annotations as a dataframe |
| GenomicAnnotationsForPREDA2GenomicAnnotations | extract the GenomicAnnotations object from the... |
| GenomicAnnotationsForPREDA2PREDAResults | add PREDA results information to genomic annotatations... |
| GenomicAnnotationsForPREDA-class | Class "GenomicAnnotationsForPREDA" GenomicAnnotations class... |
| GenomicAnnotationsForPREDAFromfile | Function to create a GenomicAnnotationsForPREDA object from a... |
| GenomicAnnotationsFromdataframe | Function to create a GenomiAnnotations object from a... |
| GenomicAnnotationsFromfile | Function to create a GenomiAnnotations object from a text... |
| GenomicAnnotationsFromLibrary | Function extracting a GenomicAnnotations object from a... |
| GenomicAnnotationsSortAndCleanNA | sort annotations according to selected chromosomes and to... |
| GenomicRegions2dataframe | extract genomic regions information as a dataframe object |
| GenomicRegionsAnnotate | extract annotations from a GenomicAnnotations object for a... |
| GenomicRegionsChrNumber | determine the number of chromosomes with genomic regions |
| GenomicRegions-class | Class "GenomicRegions" is used to manage information about... |
| GenomicRegionsComparison | compare GenomicRegions objects to identify overlaps and... |
| GenomicRegionsCreateRegionsIds | generate unique ids for GenomicRegions objects |
| GenomicRegionsFilter_neg | filter genomic regions to remove selected chromosomes |
| GenomicRegionsFilter_pos | filter genomic regions to keep selected chromosomes |
| GenomicRegionsFindOverlap | Function to find overlap between GenomicRegions objects |
| GenomicRegionsFromdataframe | Function to create a GenomiRegions object from a dataframe |
| GenomicRegionsFromfile | Function to create a GenomiRegions object from a text file |
| GenomicRegionsNumber | determine the number of genomic regions |
| GenomicRegionsSpan | determine the span of each genomic region |
| GenomicRegionsTotalSpan | determine the total span of genomic regions |
| getStatisticByName | extract data for individual analyses using the analysis name |
| MergeStatisticAnnotations2DataForPREDA | Merge a StatisticsForPREDA and a GenomicAnnotationsForPREDA... |
| PREDADataAndResults2dataframe | extract data and annotations as a dataframe with probeids as... |
| PREDADataAndResults-class | Class "PREDADataAndResults" is used to manage the PREDA... |
| PREDA_main | function performing the core of PREDA analysis |
| PREDAResults2dataframe | extact preda results statistics as a data frame object |
| PREDAResults2GenomicRegions | identify significant genomic regions from a PREDAResults... |
| PREDAResults2GenomicRegionsSingle | identify significant genomic regions from a single analysis... |
| PREDAResults2PREDADataAndResults | merge PREDAResults and input statistics to create a... |
| PREDAResults-class | Class "PREDAResults" ~is used to manage the PREDA analysis... |
| PREDAResultsGetObservedFlags | extract genomic positions with significant alterations as a... |
| preprocessingGE | Wrapper function for gene expression data preprocessing for... |
| SODEGIR_GEstatistics | Wrapper function for gene expression statistics preprocessing... |
| SODEGIRpreprocessingGE | Wrapper function for gene expression data preprocessing for... |
| StatisticsForPREDA2dataframe | extract data as a dataframe with probeids as rownames |
| StatisticsForPREDA-class | Class "StatisticsForPREDA" is used to manage the datamatrix... |
| StatisticsForPREDAFilterColumns_neg | filter statistics to remove selected analyses |
| StatisticsForPREDAFilterColumns_pos | filter statistics to keep selected analyses |
| StatisticsForPREDAFromdataframe | Function to create a StatisticsForPREDA objet from a... |
| statisticsForPREDAfromEset | function to compute a statisticsForPREDA object from an... |
| StatisticsForPREDAFromfile | Function to create a StatisticsForPREDA objet from a txt file |
